BacMap: An up-to-date electronic atlas of annotated bacterial genomes

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Cruz, Joseph ^a   Liu, Yifeng ^a   Liang, Yongjie ^a   Zhou, You ^a   Wilson, Michael ^a   Dennis, Jonathan J ^a   Stothard, Paul ^a   Van Domselaar, Gary ^b   Wishart, David S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA; TRANSFER RNA;

ARCHAEON; ARTICLE; BACMAP; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; CHROMOSOME MAP; COMPUTER GRAPHICS; GENE MAPPING; GENOMICS; INFORMATION RETRIEVAL; INFORMATION SERVICE; INTERNET; PLASMID; PRIORITY JOURNAL; PROPHAGE; WEB BROWSER;

ATLASES AS TOPIC; CHROMOSOME MAPPING; DATABASES, GENETIC; GENOME, ARCHAEAL; GENOME, BACTERIAL; MOLECULAR SEQUENCE ANNOTATION; USER-COMPUTER INTERFACE;

EID: 84862170720     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1105     Document Type: Article

References (22)

1. Fleischmann,R.D., Adams,M.D., White,O., Clayton,R.A., Kirkness,E.F., Kerlavage,A.R., Bult,C.J., Tomb,J.F., Dougherty,B.A., Merrick,J.M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
2. Fraser,C.M., Eisen,J.A., Nelson,K.E., Paulsen,I.T. and Salzberg,S.L. (2002) The value of complete microbial genome sequencing (you get what you pay for). J. Bacteriol., 184, 6403-6405. (Pubitemid 35332540)
3. Nagarajan,N. and Pop,M. (2010) Sequencing and genome assembly using next-generation technologies. Methods Mol. Biol., 673, 1-17.
4. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2011) GenBank. Nucleic Acids Res., 39, D32-D37.
5. Stothard,P. and Wishart,D.S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics, 21, 537-539. (Pubitemid 40310241)
6. Van Domselaar,G.H., Stothard,P., Shrivastava,S., Cruz,J.A., Guo,A., Dong,X., Lu,P., Szafron,D., Greiner,R. and Wishart,D.S. (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res., 33, W455-W459. (Pubitemid 44529961)
7. Carver,T., Thomson,N., Bleasby,A., Berriman,M. and Parkhill,J. (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics, 25, 119-120.
8. Krzywinski,M., Schein,J., Birol,I., Connors,J., Gascoyne,R., Horsman,D., Jones,S.J. and Marra,M.A. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
9. Soh,J., Gordon,P.M., Taschuk,M.L., Dong,A., Ah-Seng,A.C., Turinsky,A.L. and Sensen,C.W. (2008) Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking. BMC Bioinformatics, 9, 450.
10. Kanehisa,M., Goto,S., Furumichi,M., Tanabe,M. and Hirakawa,M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res., 38, D355-D360.
11. Walter,M.C., Rattei,T., Arnold,R., Güldener,U., Münsterkö tter,M., Nenova,K., Kastenmüller,G., Tischler,P., Wölling,A., Volz,A. et al. (2009) PEDANT covers all complete RefSeq genomes. Nucleic Acids Res., 37, D408-D411.
12. Sterk,P., Kulikova,T., Kersey,P. and Apweiler,R. (2007) The EMBL nucleotide sequence and genome reviews databases. Methods Mol. Biol., 406, 1-21. (Pubitemid 351367166)
13. Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Chen,Y., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2011) Ensembl 2011. Nucleic Acids Res., 39, D800-D806.
14. Davidsen,T., Beck,E., Ganapathy,A., Montgomery,R., Zafar,N., Yang,Q., Madupu,R., Goetz,P., Galinsky,K., White,O. et al. (2008) The comprehensive microbial resource. Nucleic Acids Res., 38, D340-D345.
15. Caspi,R., Altman,T., Dale,J.M., Dreher,K., Fulcher,C.A., Gilham,F., Kaipa,P., Karthikeyan,A.S., Kothari,A., Krummenacker,M. et al. (2008) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 38, D473-D479.
16. Liolios,K., Chen,I.M., Mavromatis,K., Tavernarakis,N., Hugenholtz,P., Markowitz,V.M. and Kyrpides,N.C. (2010) The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res., 38, D346-D354.
17. Gillespie,J.J., Wattam,A.R., Cammer,S.A., Gabbard,J.L., Shukla,M.P., Dalay,O., Driscoll,T., Hix,D., Mane,S.P., Mao,C. et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun., 79, 4286-4298.
18. Stothard,P., Van Domselaar,G., Shrivastava,S., Guo,A., O'Neill,B., Cruz,J., Ellison,M. and Wishart,D.S. (2005) BacMap: an interactive picture atlas of annotated bacterial genomes. Nucleic Acids Res., 33, D317-D320. (Pubitemid 40207886)
19. Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964. (Pubitemid 27298263)
20. Zhou,Y., Liang,Y., Lynch,K.H., Dennis,J.J. and Wishart,D.S. (2011) PHAST: a fast phage search tool. Nucleic Acids Res., 39, W347-W352.
21. Lima,T., Auchincloss,A.H., Coudert,E., Keller,G., Michoud,K., Rivoire,C., Bulliard,V., de Castro,E., Lachaize,C., Baratin,D. et al. (2009) HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res., 37, D471-D478.
22. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)